Taylor,
This might be due to an index file problem, which in turn may be caused by files leftover in mailboxes, from when used in an earlier version of Mail.
If your mailboxes, or at least some of them, originated in Panther, I want you to read the article at the link below, ands get back to me with some observations, before attempting any changes:
http://docs.info.apple.com/article.html?artnum=301315
This issue of leftover files applies not only to mailboxes you have previously created (which are in the Mailboxes folder the article mentioned) but can also apply to
those mailboxes in account folders created prior to the upgrade to Tiger.
It may be useful to report the size of each file or folder. Do not, however, try to list the files that are within the folder named Messages, that is found in each and every mailbox. It is very important to compare the size of any file named "mbox" with that of the Messages folder. If the mbox is greater in size than the Messages folder, then not all messages have been converted to be in the Messages folder. If no messages have ever been missed since the upgrade to Tiger, then doing anything with the mbox files may not be called for.
The path to the Mail folder is Home/Library/Mail -- within the Mail folder are one or more account folders and the Mailboxes folder.
If there are leftover files, then after removing them, (all this while Mail is not running), then you should probably remove the Envelope Index file at the root level of the Mail folder, thus forcing Mail to reindex everything, when you relaunch it. It will announce it is ready to "import" you mailboxes, but allow this to continue, and it will only be reindexing those mailboxes in the Mail folder.
Let us know if you find leftover files. If none, forcing the reindexing will be the proper step, as well.